The rust spots you show are clearly caused from paint chipping and the elements getting at them; even the bubbling where is where the water and elements get under the paint once the chip is there. That first rust spot (lighter colored) in the second picture doesn't quite look like a chip caused it; kinda more like a scratch that caused the rusting even though you state it wasn't scratched downto the metal.
Is the clearcoat thin on the sills? I've got an 11 year old tundra and the paint chips regularly occur on the exterior like your vehicle shows due to the thin clearcoat, including the bubbling effect although they haven't rusted as much since I haven't had it covered it mud/salt/water like you vehicle seems to after looking at the interior.
Is the clearcoat thin on the sills? I've got an 11 year old tundra and the paint chips regularly occur on the exterior like your vehicle shows due to the thin clearcoat, including the bubbling effect although they haven't rusted as much since I haven't had it covered it mud/salt/water like you vehicle seems to after looking at the interior.

